This may be a silly question, but this will be my first attempt to GM at Gen Con. I would like to run an RPG scenario for 6 players three different times during the con. That would count as three separate events, right? Also, would I need to submit the information about the scenario three separate times to ensure they count as three separate events?

The best way to do it is create one event, then on your EO/GM page you'll see an option to "Duplicate Event" which creates another event with identical information. Just change the start time and you're set.

Any time it's a different time or players, it's a different event, yeah. That applies for just about every time of event - it's only a single event if it's the same players in the same area for basically the entire duration.

Remember: event submissions are to inform attendees about the event, so it needs to be clear to them.